bioc-issue-bot
commented
5 days ago Hi @JINGFU9912
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: CARDspa
Title: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics
Version: 0.99.0
Date: 2024-06-25
Authors@R:
c(person(given = "Ying",
family = "Ma",
email = "ying_ma@brown.edu",
role = "aut"),
person(given = "Jing",
family = "Fu",
email = "jing_fu@brown.edu",
role = "cre"))
Description: CARD is a reference-based deconvolution method that estimates cell
type composition in spatial transcriptomics based on cell type specific
expression information obtained from a reference scRNA-seq data. A key
feature of CARD is its ability to accommodate spatial correlation in the
cell type composition across tissue locations, enabling accurate and
spatially informed cell type deconvolution as well as refined spatial map
construction. CARD relies on an efficient optimization algorithm for
constrained maximum likelihood estimation and is scalable to spatial
transcriptomics with tens of thousands of spatial locations and tens of
thousands of genes.
License: GPL-3 + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Depends: R (>= 4.3.0)
Imports: Rcpp (>= 1.0.7),RcppArmadillo,SingleCellExperiment,
SummarizedExperiment, methods, MCMCpack, fields, wrMisc, concaveman,
sp, dplyr, sf, Matrix, RANN, ggplot2, reshape2, RColorBrewer,
scatterpie, grDevices,ggcorrplot, stats, nnls, pbmcapply, RcppML, NMF,
spatstat.random, gtools
LazyData: false
biocViews: Spatial, SingleCell, Transcriptomics, Visualization
LinkingTo:
Rcpp, RcppArmadillo
Suggests:
knitr,
rmarkdown,
testthat
VignetteBuilder: knitr
URL: https://github.com/YMa-lab/CARDspa
BugReports: https://github.com/YMa-lab/CARDspa/issues
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